The decision comes two days after the young Dutchman pleaded guilty to killing Stephany Flores, a 21-year-old business student.
The court also ordered him to pay $75,000 in reparations to the victim's family, deeming the killing "cruel" and "ferocious."
Van der Sloot showed no emotion as the court clerk read the sentence, describing how he elbowed Flores in the face then beat and strangled her with his bloodied shirt. He told the court he would appeal the sentence.
It is the first ever imposed on him, despite prosecutors' repeated efforts to prove he was involved in Holloway's apparent death on the Dutch Caribbean island of Aruba.
The judges said that due to time already served, van der Sloot's sentence would end in June 2038. But under Peru's penal system, Van der Sloot could become eligible for parole after serving half of the sentence with good behavior, including work and study.
The prosecution had sought a 30-year sentence for first-degree murder and theft.
Van der Sloot's lawyer argued he killed Flores on May 30, 2010, in a fit of rage he blamed on psychological trauma from being hounded as the prime suspect in Holloway case.
The victim's father, Ricardo Flores, complained after the sentencing that Van der Sloot was living well in a Lima prison, where he has been set apart from the general population.
"A jail isn't a five-star hotel," Ricardo Flores told reporters. "Let's hope the authorities take that into account and not just in our case."
"Since the first day we've been complaining about the excessive privileges" that Van der Sloot allegedly enjoyed in jail. He said he would present evidence of that at a news conference on Monday.
Unconfirmed news reports, denied by penal authorities, say Van der Sloot has also had a television and video gaming console. As in many developing nations, foreigners with money can buy superior treatment in Peru's prisons.
The Holloway case remains open and a U.S. judge on Thursday declared her dead.
Her parents want Van der Sloot to eventually be extradited to the U.S. and tried on related charges, although Peruvian criminal law expert Luis Lamas said the law specifies that Van der Sloot must serve his time before he can be extradited.
Van der Sloot was indicted on extortion charges in Alabama the same day he was arrested for the Flores murder for allegedly accepting $25,000 in return for a promise to lead a lawyer for Holloway's mother to her daughter's remains.
Van der Sloot didn't deliver on the offer, and may have used some of that money to fly to Peru two weeks before the Flores murder.
After killing the Lima woman, he took nearly $300 in cash from Flores as well as credit cards, and was captured four days later in Chile.
Van der Sloot told police he flew into a rage when she discovered his connection to Holloway via an instant message sent to him while they were playing online poker in his hotel room.
Police forensic experts disputed that story, and the three female judges who sentenced him noted that Van der Sloot later recanted the confession, claiming it was exacted under duress and without an official translator.
The victim's family contends Van der Sloot killed Flores in order to rob her.
The imposing young man raised on a tourist island has been a staple of tabloids and true crime TV, as well as the subject of several books about Natalee Holloway.
"We've been dealing with her death for the last six and a half years," her father, Dave Holloway, said after Thursday's hearing in Birmingham, Alabama.
He said the judge's order there on his daughter's death closes one chapter in the ordeal, but added: "We've still got a long way to go to get justice."
Natalee Holloway, an 18-year-old from the wealthy Birmingham suburb of Mountain Brook, disappeared on May 30, 2005, during a high school graduation trip to Aruba, where Van der Sloot grew up.
Her body was never found and repeated searches turned up nothing even as intense media coverage brought the case worldwide attention.
Van der Sloot said he was involved in her disappearance in a videotape clandestinely made by a Dutch journalist. He later denied it, however, and has told several interviewers that he is a pathological liar.
A homicide investigation into Holloway's death remains open in Aruba though there has been no recent activity, said Solicitor General Taco Stein, an official with the prosecutor's office in Aruba.
There is no indication U.S. officials have moved to seek to extradite Van der Sloot; Peru's Foreign Ministry said this week that it has no U.S. extradition request for him.
No members of Van der Sloot's family attended the trial in Peru. His lawyer said the defendant's mother, Anita, did not want the media attention.
The defendant's father, a prominent lawyer, died of a heart attack at age 57 in February 2010.
